General course information
Schedule
| Day | Date | Time | Room | Topic | Lecturer |
|---|---|---|---|---|---|
| Mon | 13.10.2025 | 12:00-14:00 | S09 | Introduction to course | Schmid |
| Tue | 14.10.2025 | 10:00-12:00 | S09 | Working with scientific literature - 1 | Schmid |
| Mon | 20.10.2025 | 12:00-14:00 | PC Room 3 | Introduction to data science and R (Part I) | Thorwarth |
| Tue | 21.10.2025 | 10:00-12:00 | S09 | Working with scientific literature - 2 | Schmid |
| Mon | 27.10.2025 | 12:00-14:00 | PC Room 3 | Introduction to R (Part 2) | Daware |
| Tue | 28.10.2025 | 10:00-12:00 | S09 | Scientific measurements and estimation | Daware |
| Mon | 03.11.2025 | 12:00-14:00 | PC Room 3 | Tools for reproducible research | Daware |
| Tue | 04.11.2025 | 10:00-12:00 | S09 | Visualization of scientific data | Daware |
| Mon | 10.11.2025 | 12:00-14:00 | PC Room 3 | Cleaning and processing of scientific data | Daware |
| Tue | 11.11.2025 | 10:00-12:00 | S09 | What is science? | Schmid |
| Mon | 17.11.2025 | 12:00-14:00 | S09 | The scientific method | Schmid |
| Tue | 18.11.2025 | 10:00-12:00 | S09 | Scientific reasoning: General rules | Schmid |
| Mon | 24.11.2025 | 12:00-14:00 | S09 | Scientific reasoning: Common errors | Schmid |
| Tue | 25.11.2025 | 10:00-12:00 | S09 | Limits of science and pseudoscience | Schmid |
| Mon | 01.12.2025 | 12:00-14:00 | S09 | Experimental design 1 | Thorwarth |
| Tue | 02.12.2025 | 10:00-12:00 | S09 | Experimental design 2 | Thorwarth |
| Mon | 08.12.2025 | 12:00-14:00 | S09 | No class (Preparation of presentations) | |
| Tue | 09.12.2025 | 10:00-12:00 | S09 | Scientific reasoning with probabilities, Presentations | Schmid |
| Mon | 15.12.2025 | 12:00-14:00 | S09 | Statistical testing - Bayesian inference, Presentations | Schmid |
| Tue | 16.12.2025 | 10:00-12:00 | S09 | Student Presentations, Course feedback | Schmid |
| End of year break | |||||
| Mon | 12.01.2026 | 12:00-14:00 | S09 | Statistical testing - Frequentist inference, Presentations | Schmid |
| Tue | 13.01.2026 | 10:00-12:00 | S09 | Models and model selection, Presentations | Schmid |
| Mon | 19.01.2026 | 12:00-14:00 | S09 | Publishing and patenting in science, Presentations | Schmid |
| Tue | 20.01.2026 | 10:00-12:00 | S09 | Ethics in scientific research, Presentations | Schmid |
| Mon | 26.01.2026 | 12:00-14:00 | S09 | Rules for good research practice , Presentations | Schmid |
| Tue | 27.01.2026 | 10:00-12:00 | S09 | Science and the public, Presentations | Schmid |
| Mon | 09.02.2026 | 08:30-17:00 | Final (oral) exams (Exam Period 1) | Schmid | |
| Tue | 10.02.2026 | 08:30-17:00 | Final (oral) exams (Exam Period 1) | Schmid | |
| Wed | 01.04.2026 | 09:00-11:00 | Final (oral) exams (Exam Period 2) | Schmid |
Course lecturers
Prof. Dr. Karl Schmid
- Professor of Crop Biodiversity and Breeding Informatics
- Office hours: Wednesday, 13:00 - 14:00 or by appointment
- Contact: karl.schmid@uni-hohenheim.de
- Research: Population Genetics of Wild and Crop Plants
- Webpage: http://evoplant.uni-hohenheim.de
Dr. Patrick Thorwarth
- Head of State Breeding Institute
- Contact: patrick.thorwarth@uni-hohenheim.de
Dr. Anurag Daware
- Postdoc in the research group Crop Biodiversity and Breeding Informatics
- Contact: anuragvasantrao.daware@uni-hohenheim.de
Course organisation
Coursework
- You need to submit one declaration of plagiarism (Link) that covers both courseworks
- All documents are to be uploaded on ILIAS - Link to be added
Coursework 1: Summary of a review paper or book chapter
Coursework 2: Small data analysis project
Course topic
Introduction to course
- Welcome to Crop Science Master Program (Ivan Guzman and Karl Schmid)
- Introduction to course: Organisation and topics (Lecture notes)
Working with scientific literature: Outlining, citing, plagiarism
In class
- Lecture on outlining, citing and plagiarism (Lecture notes)
- Plagiarism exercise: Link
Introduction to data science and R (Part 1)
Before class
Installation R, R Studio and Quarto on your own computer:
- Download and install R: http://cran.r-project.org
- Download and install RStudio: http://www.rstudio.com/products/rstudio/download/
- Download and install Quarto: https://quarto.org/docs/download/index.html
If you encounter problems with your installation, please post questions (including error messages or screenshots) to the forum!
In class
- Lecture notes: Introduction to data science
- R introduction tutorial: Link
Additional material for self-study
- Introduction to the Quarto publishing system:
- Wickham and Grolemund: R for Data Science, 2nd edition HTML version of the book
Working with scientific literature 2: Quality and searching
Before class
- Read the short opinion article by Stam and McDonald: PDF
In class
- An exercise in outlining based on the article of Stam and McDonald
- World Café and subsequent discussion on the quality and impact of scientific literature (Lecture notes)
- If time permits: Short demonstration of Google Scholar, Research Rabbit and reference management with Zotero
Introduction to R - Part 2
In class
Continuation from previous computer lab.
- R introduction tutorial: Link
Scientific measurements and estimation
Before class
- No preparation needed!
In class
- Lecture on measurement - Lecture notes
- Exercise on measurements- Link
Tools for reproducible research
In class
- Lecture on introduction to data science - Lecture notes and on reproducible research - Lecture notes
- Computer Lab: qmd File | HTML
Visualization of scientific data
Before class
- Lecture: Slides | Lecture videos: Visualization-1 (15 min) Visualization-2 (22 min) Visualization-3 (18 min) | Lecture notes
In class
Cleaning and processing of scientific data
Before class
In class (Computer lab):
- Required R packages: tidyverse, ggplot2
- Data: preg.csv, preg2.csv, preg4.csv, pew.csv
- Computerlab: qmd File | HTML
What is science?
Before class
In class
- Short lecture on the history of science philosophy Lecture notes
- Group discussion of Okasha, Philosopy of Science, Chapter 1
The scientific method
Before class
In class
- Short lecture on the scientific method. Lecture notes
- Discuss questions on Okasha, Philosopy of Science, Chapter 2
Scientific reasoning: General rules
Before class
No preparation for this class!
In class
- Lecture on the scientific method. Lecture notes
- Discussions on lecture topic
Scientific reasoning: Common errors
Before class
- Videos: Fallacies in deductive reasoning (17 min) Inductive reasoning (Total 30 min; start at minute 22:00)
- Slides: PDF
- Lecture notes: HTML
In class
- Short repetition of errors in scientific reasoning
- Group discussion on key fallacies and errors in scientific reasoning: PDF
Limits of science and pseudoscience
Before class
In class
- Lecture on limits of science and pseudoscience | Lecture notes
- Discussion of paper on eurythmic treatment of apples?: Good science, bad science or pseudoscience? Questions for discussion are here
Additional material:
- What is biodynamic agriculture? Youtube (German TV; 11 min; Use automatic translation in the settings)
- Portrait of the Reyerhof, a biodynamic farm in Stuttgart-Möhringen Youtube (German TV; start at 4:20; In German only)
Experimental design 1: Hypotheses and designs
Before class
- Watch introductory videos: Introduction (9 min) | History and basic principles (18 min) | Design and planning (17 min) | Slides: PDF
- Or, read the lecture notes on experimental design: Link
- Or, read the chapter about selecting the broad design of a study in Ruxton and Colgreave: Experimental Design for the Life Sciences (4th Ed) 2016, Chapter 3
In class
- Short lecture with discussions on topics related to hypotheses
- Group discussion of use cases on experimental design: Link
Experimental design 2: Variation and pseudoreplication
Before class
- Read Ruxton and Colgreave: Experimental Design for the Life Sciences (4th Ed) 2016, Chapter 4 :::
In class
- Short lecture with discussions on variation and pseudoreplication
- Group discussion of use cases on experimental design: Link
Experimental design 3: Types of experimental designs
Before class
In class
- Short review of experimental designs based on the assigned literature
- Group discussion of use cases on experimental design: Link
Experimental design 4: Blocking and other considerations
Before class
- Read about the concept of blocking in Ruxton and Colgreave: Experimental Design for the Life Sciences (4th Ed) 2016, Chapter 9 (9.1 and 9.2)
In class
- Short lecture on topics related to blocking
- Group discussion of use cases on experimental design: Link
Scientific reasoning with probabilities
Before class
- Slides | Videos: Introduction (19 min) | Formal definition (16 min) | Bayes’ Theorem (18 min)
- Lecture notes
In class
- Recapitulation and discussion of key concepts
- In class discussion exercises: HTML
Statistical testing
Before class
- Statistical testing: Slides | No video | Lecture notes
In class
- Lecture on statistical testing
- Discussion of problems
- Computer demonstration: Introduction to Bayesian analysis qmd | HTML
Models and model selection
Before class
In class
- Recapitulation of key concepts
- In class discussion of exercises
Publishing and patenting in science
Before class
- Scientific publishing: Slides | Videos: Publishing-1 (17 min) Publishing-2 (9 min) Publishing-3 (20 min) | Lecture notes
- Patenting : Slides | Videos: Patents-1 (26 min) Patents-2 (15 min) Patents-3 (9 min) | Lecture notes
In class
- Scientific publishing: Discussion questions
- Patenting: Discussion questions
Ethics in scientific research
Before class
- Ethics in scientific research:
- Slides | No video! | Lecture notes
- TED talk on the dignity of plants (YouTube) (15 min) - Will discuss in class
- Discussion questions for the TED talk: Link
In class
- Short introductory lectures on ethics
- Discussion questions on ethics in science and dignity of plants based on the TED video
Rules for good research practice
Before class
- Good research practice: Slides | No video! | Lecture notes
- DFG code of conduct for good research practice: Link
In class
- Short introductory lecture on good research practice
- Discussion of DFG Rules for research practice
- Discussions of problems related to good research practice: PDF
Science and the public
Before class:
- Slides | Video (22 min) | Lecture notes
- TED Talk on the engineering of our food (YouTube) (18 min)
In class
- Short lecture
- Discussion of TED talk: Questions as PDF